Again, the difference is not in the makeup of the particles, but in the space between the particles in orbit (electrons) and the nucleus (with protons).
There are only a little over 100 atoms in all the Universe that we know of. All that we see is built out of these and out of a combination of these. All atoms are made up of protons, electrons and neutrons, except hydrogen which has no neutron. No atom is different than the other except in number: Helium, Calcium, Titanium, Tin, whatever; they are all the same thing . . .except in number.

They follow an orderly mathematical progression. Dimitry Mendeleyev noted that Indian Sanskrit grammarian Panini who could think about this progression in alphabets of a language 7000 years ago . Hydrogen, the simplest atom, has 1 proton in the nucleus and 1 electron in orbit. Helium has 2. 3 protons in the nucleus and 3 electrons in orbit is no longer a gas, it is like magic Lithium, a silver-white light weight metal of atomic number 3 . It goes on and on to Seaborgium, with 106 protons in the nucleus and electron configuration 2-8-18-32-32-12-2.

Therefore, the difference between all matter is electromagnetic energy created by the different number of these charged particles, not in the basic make up of these particles as individuals. The reason Nitrogen and Oxygen are such different gases cannot be that Nitrogen has 7 protons and 7 electrons and that Oxygen has 8 of each. Hence it is the different amount of electromagnetic energy that that one proton and one electron make that changes the substance.

The understanding of chemical bonding has been fundamentally transformed by quantum mechanics, as in Schrödinger's wave equations. New fields in physics emerged after Newtons ideas were discarded into the dustbin of history , in favour of quantum mechanics and relativity — solid-state physics, condensed-matter physics, superconductivity, nuclear physics, and elementary particle physics— all of these found a consistent basis in quantum mechanics. No fundamental deficiencies have been found in quantum mechanics, since the past 7 decades.

Again, the difference is not in the makeup of the particles, but in the space between the particles in orbit (electrons) and the nucleus (with protons).

That space is the substance of everything. That space is electromagnetic energy. That space is “reality.”
That space is the atom. Electromagnetism is the substance of everything. In essence, that “space” is the substance of all structure.

The electrons, protons and neutrons are only a small part of the atom. It is the space between them that is, ironically, the “substance.”

Within the electromagnetic force of the atom is the key to everything: creation, transmutation . . .limitless power.